Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,117,071	T→C	F44S (TTC→TCC)	rpmE →	50S ribosomal protein L31

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,117,071	0	T	C	100.0%	131.3 / NA	38	F44S (TTC→TCC)	rpmE	50S ribosomal protein L31
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/20);  total (18/20)

CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGC  >  NZ_CP009273/4116985‑4117147                                                                                       |                                                                             ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                           <  1:293317/90‑1 (MQ=255) ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                           <  1:890814/90‑1 (MQ=255)       ttGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaa                                                                     <  2:734636/90‑1 (MQ=255)         gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                   <  2:787219/90‑1 (MQ=255)         gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                   <  2:681202/90‑1 (MQ=255)           ggTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAg                                                                 >  2:21486/1‑90 (MQ=255)           ggTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAg                                                                 <  2:511556/90‑1 (MQ=255)               aCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTg                                                             <  1:657699/90‑1 (MQ=255)               aCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTg                                                             <  2:201204/90‑1 (MQ=255)                cGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGa                                                            <  1:572332/90‑1 (MQ=255)                cGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGa                                                            <  1:172207/90‑1 (MQ=255)                      gAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                      <  1:686062/90‑1 (MQ=255)                      gAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                      <  2:226638/90‑1 (MQ=255)                          aTCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTAcc                                                  >  2:838506/1‑90 (MQ=255)                           tCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCg                                                 <  1:523391/90‑1 (MQ=255)                              gCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTg                                              >  2:462994/1‑90 (MQ=255)                              gCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTg                                              >  2:844228/1‑90 (MQ=255)                                tCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGc                                            <  1:1189033/90‑1 (MQ=255)                                tCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGc                                            <  1:194170/90‑1 (MQ=255)                                 ccACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGcc                                           >  2:121715/1‑90 (MQ=255)                                      gTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGtt                                      >  2:370883/1‑90 (MQ=255)                                         ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                   <  2:661232/90‑1 (MQ=255)                                             aTGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCt                               >  2:768449/1‑90 (MQ=255)                                             aTGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCt                               >  2:481724/1‑90 (MQ=255)                                                   tGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                      <  1:917679/61‑1 (MQ=255)                                                   tGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                      >  2:917679/1‑61 (MQ=255)                                                   tGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaaca                         >  2:923458/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                      <  1:982298/60‑1 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                      >  2:982298/1‑60 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                        >  1:307488/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                        >  2:785305/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                        >  2:894468/1‑90 (MQ=255)                                                         tCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGtt                   >  1:1067101/1‑90 (MQ=255)                                                           gACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTc                 >  1:945118/1‑90 (MQ=255)                                                            aCGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCa                <  2:1218181/90‑1 (MQ=255)                                                                       aaGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgc     <  2:1067101/90‑1 (MQ=255)                                                                          tGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc  >  1:245177/1‑90 (MQ=255)                                                                          tGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc  >  2:91576/1‑90 (MQ=255)                                                                                       |                                                                             CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGC  >  NZ_CP009273/4116985‑4117147

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑